Genome of wild olive and the evolution of oil biosynthesis

Here we present the genome sequence and annotation of the wild olive tree (Olea europaea var. sylvestris), called oleaster, which is considered an ancestor of cultivated olive trees. More than 50,000 protein-coding genes were predicted, a majority of which could be anchored to 23 pseudochromosomes o...

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Published in:	Proceedings of the National Academy of Sciences - PNAS Vol. 114; no. 44; pp. E9413 - E9422
Main Authors:	Unver, Turgay, Wu, Zhangyan, Sterck, Lieven, Turktas, Mine, Lohaus, Rolf, Li, Zhen, Yang, Ming, He, Lijuan, Deng, Tianquan, Escalante, Francisco Javier, Llorens, Carlos, Roig, Francisco J., Parmaksiz, Iskender, Dundar, Ekrem, Xie, Fuliang, Zhang, Baohong, Ipek, Arif, Uranbey, Serkan, Erayman, Mustafa, Ilhan, Emre, Badad, Oussama, Ghazal, Hassan, Lightfoot, David A., Kasarla, Pavan, Colantonio, Vincent, Tombuloglu, Huseyin, Hernandez, Pilar, Mete, Nurengin, Cetin, Oznur, Van Montagu, Marc, Yang, Huanming, Gao, Qiang, Dorado, Gabriel, Van de Peer, Yves
Format:	Journal Article
Language:	English
Published:	United States National Academy of Sciences 31-10-2017
Series:	PNAS Plus
Subjects:	Accumulation Annotations Biological Evolution Biological Sciences Biosynthesis Biosynthetic Pathways - genetics Crops Desaturation Divergence Evolution FAD2 gene Fatty Acid Desaturases - genetics Fatty acids Fruit trees Gene duplication Gene expression Gene Expression - genetics Gene families Genes Genome, Plant - genetics Genomics Linoleic Acids - genetics Nucleotide sequence Oils - metabolism Olea - genetics Olea - metabolism Olea europaea sylvestris Oleic acid Oleic Acid - genetics Olive oil Olives PNAS Plus Reproduction (copying) RNA, Small Interfering - genetics siRNA Transposons Trees fatty-acid biosynthesis oil crop polyunsaturated fatty-acid pathway whole-genome duplication siRNA regulation
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Summary:	Here we present the genome sequence and annotation of the wild olive tree (Olea europaea var. sylvestris), called oleaster, which is considered an ancestor of cultivated olive trees. More than 50,000 protein-coding genes were predicted, a majority of which could be anchored to 23 pseudochromosomes obtained through a newly constructed genetic map. The oleaster genome contains signatures of two Oleaceae lineage-specific paleopolyploidy events, dated at ∼28 and ∼59 Mya. These events contributed to the expansion and neofunctionalization of genes and gene families that play important roles in oil biosynthesis. The functional divergence of oil biosynthesis pathway genes, such as FAD2, SACPD, EAR, and ACPTE, following duplication, has been responsible for the differential accumulation of oleic and linoleic acids produced in olive compared with sesame, a closely related oil crop. Duplicated oleaster FAD2 genes are regulated by an siRNA derived from a transposable element-rich region, leading to suppressed levels of FAD2 gene expression. Additionally, neofunctionalization of members of the SACPD gene family has led to increased expression of SACPD2, 3, 5, and 7, consequently resulting in an increased desaturation of steric acid. Taken together, decreased FAD2 expression and increased SACPD expression likely explain the accumulation of exceptionally high levels of oleic acid in olive. The oleaster genome thus provides important insights into the evolution of oil biosynthesis and will be a valuable resource for oil crop genomics.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Reviewers: R.M., University of Illinois at Urbana–Champaign; and K.S., MPI for Plant Breeding Research. 1T.U. and Z.W. contributed equally to this work. Contributed by Marc Van Montagu, September 11, 2017 (sent for review May 26, 2017; reviewed by Ray Ming and Korbinian Schneeberger) 2Present address: Egitim Mah, Ekrem Guer Sok, No:26/3, 35340 Balcova, Izmir, Turkey. Author contributions: T.U., M.V.M., G.D., and Y.V.d.P. designed research; T.U., Z.W., L.S., M.T., R.L., Z.L., M.Y., F.J.E., C.L., F.J.R., E.D., F.X., B.Z., O.B., H.G., D.A.L., P.K., V.C., H.T., P.H., N.M., O.C., G.D., and Y.V.d.P. performed research; T.U., Z.W., L.S., M.T., R.L., Z.L., M.Y., F.J.E., C.L., F.J.R., E.D., F.X., B.Z., O.B., H.G., D.A.L., P.K., V.C., H.T., P.H., N.M., O.C., G.D., and Y.V.d.P. analyzed data; T.U., L.S., R.L., G.D., and Y.V.d.P. wrote the paper; Z.W., M.T., M.Y., L.H., T.D., I.P., A.I., S.U., M.E., E.I., N.M., H.Y., and Q.G. contributed data production; and T.U., G.D., and Y.V.d.P. contributed to the project leadership.
ISSN:	0027-8424 1091-6490 1091-6490
DOI:	10.1073/pnas.1708621114